We present a study of several mixtures obtained by the mixing of two organic acetate-based salts (choline acetate, ChAc, or tetrabutylammonium acetate, TBAAc) with three different natural organic acids (ascorbic acid, AA, citric acid, CA, and maleic acid, MA). The structures of the starting materials and of the mixtures were characterized by infrared spectroscopy (FT-IR) and classic molecular dynamics simulations (MD). The thermal behavior was characterized by differential scanning calorimetry (DSC) and thermogravimetry analysis (TGA). The obtained mixtures, especially the ChAc-based ones, strongly tend to vitrify at low temperatures and are stable up to 100-150 °C. The FTIR measurements suggest the formation of a strong H-bond network: the coordination between acids and ChAc or TBAAc takes place by the donation of the H-bond by the acids to the oxygen of the acetate anion, which acts as an acceptor (HBA). The comparison with MD analysis indicates that acids predominantly exploit their more acidic hydrogens. In particular, we observe the progressive shift of νC═O and νOH when the ratios of acids increase. The structural differences between the two studied cations influence the spatial distribution of the components in the mixture bulk phases. In particular, the analysis of the theoretical structure function I(q) of the TBAAc-based systems shows the presence of important prepeaks at low q, a sign of the formation of apolar domain, due to the nanosegregation of the alkyl chains.